[DiapDealer]

I'm not fond of popups that show once and are then (usually) dismissed forever. It's too easy to forget that a choice was made, and too hard to unmake it if one wants to.

Seems to me that you're basically asking for a preference setting to automatically restructure all epubs upon opening. What would be the advantage of a popup over a regular preference choice?

I'm just not sure how feasible such an option is.

Have you asked the author of the plugin(s) if they could update them to work with any and all possible epub structures? Many of them already do, after all. The Restructure tool was initially intended to give plugin devs time to update their plugins to match Sigil's new capabilities. I'm not really keen on the notion of modifying Sigil in a way that makes it easier for them to never do so.